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Why so little specificity in mtdna studies?

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  • Why so little specificity in mtdna studies?

    Dienekes posted a study today which illustrates one of my pet-peeves, which is little or no specificity when mtdna is mentioned in a study:
    http://dienekes.blogspot.com/2013/12...ian-mtdna.html

    Dienekes quotes the paper:
    Our approach clearly identified six different mitochondrial lineages (corresponding to five distinct haplogroups: J, H, K, X2 and W) among eight human remains, indicating noticeable mitochondrial diversity. During this period, the site might have been the cemetery for a social group with significant genetic diversity.
    Really? Just J, H, and K...wouldn't it be more interesting to nail down the subclades just a bit more? Is there some reason why mtdna studies tend to be so general?

    I tried to find out more from the study but it seems to be behind a pay wall or sign in:
    http://www.sciencedirect.com/science...05440313003191

  • #2
    Originally posted by Littlest bit View Post
    Dienekes posted a study today which illustrates one of my pet-peeves, which is little or no specificity when mtdna is mentioned in a study:
    http://dienekes.blogspot.com/2013/12...ian-mtdna.html

    Dienekes quotes the paper:

    Really? Just J, H, and K...wouldn't it be more interesting to nail down the subclades just a bit more? Is there some reason why mtdna studies tend to be so general?
    They were able to get only HVR1 details. Even for HVR1, they were only able to get partial results for one sample. The haplogroups are based on HVR1. To actually nail down the sub-clade, you need HVR1+HVR2+Coding region in most cases.

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    • #3
      They were able to get only HVR1 details. Even for HVR1, they were only able to get partial results for one sample. The haplogroups are based on HVR1. To actually nail down the sub-clade, you need HVR1+HVR2+Coding region in most cases.
      Right, but why is it only HVR1? Is it technically impossible to go deeper on these old samples or are these researchers naive to the many subclades of these branches, which could prove to be quite interesting if known? In addition, "J, H, K, X2 and W" does not prove "significant genetic diversity" since you can find all of those branches in virtually any European country today. The cemetery in question only dates to 7th-8th century A.D. which, in mitochondrial DNA time, is not very long ago.
      http://www.eupedia.com/europe/europe...requency.shtml

      I don't know, it just seems like I've been floating around these forums since 2009 and most of these mtdna studies seem no more informative than they were back then. Just vague claims based on branch designations. Autosomal DNA studies have been revolutionized since 2009 and Y chromosome tests are promising to rewrite the whole understanding of the Y and yet mtdna studies are still just as primitive as before. Why can't they be more specific? Lack of interest or technically impossible?

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      • #4
        Originally posted by Littlest bit View Post
        Dienekes posted a study today which illustrates one of my pet-peeves, which is little or no specificity when mtdna is mentioned in a study:
        http://dienekes.blogspot.com/2013/12...ian-mtdna.html

        Dienekes quotes the paper:


        Really? Just J, H, and K...wouldn't it be more interesting to nail down the subclades just a bit more? Is there some reason why mtdna studies tend to be so general?

        I tried to find out more from the study but it seems to be behind a pay wall or sign in:
        http://www.sciencedirect.com/science...05440313003191
        Littlest bit...I'd like to know too. Thanks for bringing this forward.

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        • #5
          There have been several studies published in the last two years in which they did test the full mtDNA sequence for ancient samples, (papers by Fu et al.; Brotherton et al; Brandt et al; and Bollinger et al.) The results of these studies have been much more informative, and this also shows that it is possible to do the full sequence routinely for ancient mtDNA. And of course, we have the recent paper on the full mtDNA sequence for a 300,000 year old archaic human.

          Hopefully the authors of this paper will also go on to do the full sequence. I think it is a waste of sample material if they only test the HVR.

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          • #6
            there is also another study that has not received too much attention http://dx.doi.org/10.1016/j.ajhg.2013.10.002

            In the supplementary tables - Table S1 page 8 gives a lot of information as to which samples where subject successful extraction and which not.
            Some samples where able to produce FMS data

            I hope that the method they put froward will improve the mtDNA extraction success rate of ancient bones and lower the cost (as they are stating in the study)

            Gail, I have identified that sample T2G2 from this study is on genetic distance 1 - from FTDNA kit N112116 (Genbank accession - KC765916). N112116 has one mutation more at 14577C.

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